enhanced Green's Function Reaction Dynamics

An event-driven algorithm for simulating reaction-diffusion systems at the particle level

GFRD decomposes the many-body reaction-diffusion problem into one- and two-body problems that can be solved analytically using Green’s Functions [1,2,3,4]. These Green’s Functions are then employed to set up an event-driven algorithm, which makes it possible to take large jumps in time and space when the particles are far apart from each other. GFRD can be up to 6 orders of magnitude faster than conventional algorithms based on Brownian Dynamics [1].

Movie 1. eGFRD in action.

Applications

The eGFRD algorithm is generic and can be applied to a wide variety of reaction-diffusion problems, including those in population dynamics, evolution, and soft-condensed matter physics. The scheme presented here has been specifically designed to simulate biochemical networks.

eGFRD in all dimensions

The original code to simulate reactions and diffusion in 3D (cytoplasm) has been rewritten in Modern C++, resulting in a very fast simulator. A prototype has been developed that can also simulate systems in 2D (membranes) and 1D (filaments) [5].

Developers

The eGFRD algorithm was originally developed by the group of Takahashi at the Riken institute in Japan and the group of Ten Wolde at AMOLF in The Netherlands.